import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
import jalview.io.HTMLOutput;
import jalview.jbgui.GAlignmentPanel;
import jalview.math.AlignmentDimension;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
-import java.awt.Insets;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
private IdPanel idPanel;
- private boolean headless;
-
IdwidthAdjuster idwidthAdjuster;
- /** DOCUMENT ME!! */
public AlignFrame alignFrame;
private ScalePanel scalePanel;
private AnnotationLabels alabels;
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
-
private int hextent = 0;
private int vextent = 0;
alignFrame.updateEditMenuBar();
- paintAlignment(true);
+ // no idea if we need to update structure
+ paintAlignment(true, true);
}
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
- if (this.alignFrame.getSplitViewContainer() != null)
- {
- ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
- }
-
repaint();
}
{
boolean scrolled = scrollToPosition(results, 0, true, false);
- boolean noFastPaint = scrolled && av.getWrapAlignment();
+ boolean fastPaint = !(scrolled && av.getWrapAlignment());
- getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
+ getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
}
/**
if (av.hasHiddenColumns())
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- start = hidden.findColumnPosition(start);
- end = hidden.findColumnPosition(end);
+ start = hidden.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(end);
if (start == end)
{
if (!hidden.isVisible(r[0]))
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
+ paintAlignment(redrawOverview, false);
return scrollNeeded;
}
}
validateAnnotationDimensions(true);
addNotify();
- paintAlignment(true);
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, false);
}
/**
/*
* Estimate available height in the AlignFrame for alignment +
* annotations. Deduct an estimate for title bar, menu bar, scale panel,
- * hscroll, status bar (as these are not laid out we can't inspect their
- * actual heights). Insets gives frame borders.
+ * hscroll, status bar, insets.
*/
- int stuff = Platform.isAMac() ? 80 : 100;
- Insets insets = alignFrame.getInsets();
- int availableHeight = alignFrame.getHeight() - stuff - insets.top
- - insets.bottom;
+ int stuff = Platform.isAMac() ? 120 : 140;
+ int availableHeight = alignFrame.getHeight() - stuff;
/*
* If not enough vertical space, maximize annotation height while keeping
}
else
{
- int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+ int widthInRes = (canvasWidth / av.getCharWidth());
int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
- / av.getCharHeight()) - 1;
+ / av.getCharHeight());
ranges.setViewportWidth(widthInRes);
ranges.setViewportHeight(heightInSeq);
{
// reset the width to exclude hidden columns
width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
+ .absoluteToVisibleColumn(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
}
ranges.setViewportStartAndHeight(y, height);
}
- if (!fastPaint)
- {
- repaint();
- }
+ repaint();
}
/**
repaint();
}
- /**
- * Repaint the alignment including the annotations and overview panels (if
- * shown).
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
*/
@Override
- public void paintAlignment(boolean updateOverview)
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
av.getSortAnnotationsBy());
repaint();
- if (updateOverview)
+ if (updateStructures)
{
- // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
@Override
public void paintComponent(Graphics g)
{
- invalidate();
+ invalidate(); // needed so that the id width adjuster works correctly
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
+
+ validate(); // needed so that the id width adjuster works correctly
/*
- * set scroll bar positions
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
*/
ViewportRanges ranges = av.getRanges();
setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int resWidth = getSeqPanel().seqCanvas
return idwidth.intValue() + 4;
}
- void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+ /**
+ * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
+ * writes it to the specified file
+ *
+ * @param type
+ * @param file
+ */
+ void makeAlignmentImage(ImageMaker.TYPE type, File file)
{
- int boarderBottomOffset = 5;
- long pSessionId = System.currentTimeMillis();
- headless = (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"));
- if (alignFrame != null && !headless)
- {
- if (file != null)
- {
- alignFrame.setProgressBar(MessageManager
- .formatMessage("status.saving_file", new Object[]
- { type.getLabel() }), pSessionId);
- }
- }
- try
+ final int borderBottomOffset = 5;
+
+ AlignmentDimension aDimension = getAlignmentDimension();
+ // todo use a lambda function in place of callback here?
+ ImageWriterI writer = new ImageWriterI()
{
- AlignmentDimension aDimension = getAlignmentDimension();
- try
+ @Override
+ public void exportImage(Graphics graphics) throws Exception
{
- jalview.util.ImageMaker im;
- final String imageAction, imageTitle;
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- imageAction = "Create PNG image from alignment";
- imageTitle = null;
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- imageAction = "Create EPS file from alignment";
- imageTitle = alignFrame.getTitle();
- }
- else
- {
- imageAction = "Create SVG file from alignment";
- imageTitle = alignFrame.getTitle();
- }
-
- im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(),
- aDimension.getHeight() + boarderBottomOffset, file,
- imageTitle, alignFrame, pSessionId, headless);
- Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
- if (graphics != null)
- {
- printWrappedAlignment(aDimension.getWidth(),
- aDimension.getHeight() + boarderBottomOffset, 0,
- graphics);
- im.writeImage();
- }
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + borderBottomOffset, 0, graphics);
}
else
{
- if (graphics != null)
- {
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- graphics, graphics);
- im.writeImage();
- }
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
}
-
- } catch (OutOfMemoryError err)
- {
- // Be noisy here.
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- // System.out.println("Create IMAGE: " + err);
- } catch (Exception ex)
- {
- ex.printStackTrace();
}
- } finally
- {
+ };
- }
+ String fileTitle = alignFrame.getTitle();
+ ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
+ fileTitle);
+ int imageWidth = aDimension.getWidth();
+ int imageHeight = aDimension.getHeight() + borderBottomOffset;
+ String of = MessageManager.getString("label.alignment");
+ exporter.doExport(file, this, imageWidth, imageHeight, of);
}
+ /**
+ * Calculates and returns a suitable width and height (in pixels) for an
+ * exported image
+ *
+ * @return
+ */
public AlignmentDimension getAlignmentDimension()
{
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth);
+ .absoluteToVisibleColumn(maxwidth);
}
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
if (av.getWrapAlignment())
{
height = getWrappedHeight();
- if (headless)
+ if (Jalview.isHeadlessMode())
{
// need to obtain default alignment width and then add in any
// additional allowance for id margin
}
- /**
- * DOCUMENT ME!
- */
- public void makeEPS(File epsFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makePNG(File pngFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
- }
-
- public void makeSVG(File svgFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
- }
-
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
if (av.hasHiddenColumns())
{
maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int height = ((maxwidth / chunkWidth) + 1) * cHeight;
if (annotationPanel != null)
{
annotationPanel.dispose();
+ annotationPanel = null;
}
if (av != null)
{
av.removePropertyChangeListener(propertyChangeListener);
- jalview.structure.StructureSelectionManager ssm = av
- .getStructureSelectionManager();
+ propertyChangeListener = null;
+ StructureSelectionManager ssm = av.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
ssm.removeCommandListener(av);
*/
protected void closeChildFrames()
{
+ if (overviewPanel != null)
+ {
+ overviewPanel.dispose();
+ overviewPanel = null;
+ }
if (calculationDialog != null)
{
calculationDialog.closeFrame();
+ calculationDialog = null;
}
}
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- /*
- * To avoid jumpy vertical scrolling (if some sequences are gapped or not
- * mapped), we can make the scroll-to location a sequence above the one
- * actually mapped.
- */
- SequenceI mappedTo = sr.getResults().get(0).getSequence();
- List<SequenceI> seqs = av.getAlignment().getSequences();
-
- /*
- * This is like AlignmentI.findIndex(seq) but here we are matching the
- * dataset sequence not the aligned sequence
- */
- boolean matched = false;
- for (SequenceI seq : seqs)
- {
- if (mappedTo == seq.getDatasetSequence())
- {
- matched = true;
- break;
- }
- }
- if (!matched)
- {
- return; // failsafe, shouldn't happen
- }
-
- /*
- * Scroll to position but centring the target residue.
- */
scrollToPosition(sr, verticalOffset, true, true);
}
if (adjustHeight)
{
// sort, repaint, update overview
- paintAlignment(true);
+ paintAlignment(true, false);
}
else
{
git://source.jalview.org / jalview.git / blobdiff